Only one Emperor’s Standard (yellow with black eagle with maps in his
claws) existed in times of Catherine the Great. She used it.
Kostroma (city on Volga River) have the arms:
«Azure, a ship of Catherine the Great with Emperor’s Standard on
main-mast».Victor Lomantsov, 02 Jun 2000

Russian Imperial Army Regimental "Color" Banner of One of the
Life-Guards' Regiments From the Reign of Pavel I, Circa 1800.Source: http://www.ebay.com/itm/370727819973
Description:
The silk banner roughly square, the center with the Imperial
double-headed eagle in semi-profile with one raised wing and one
lowered wing and with lightning bolts in its talons, set within ribbon
tied laurel wreaths beneath the devices "God is with us" and "Bliss"
and surmounted by the Imperial crown, the corners with the mirror
Russian/Maltese monograms, also within ribbon-tied laurel wreaths.
Measurements: 56 ½ x 57 ½ in.; 144 x 146 cm
In 1797, Emperor Paul I instituted a large scale reform of the Russian
army and government that had important implications for Russian
heraldry and military regalia. Among these changes was the institution
of new types of banners for military regiments. Every Life-Guards'
Regiment received one "White" and several "Color" banners of new
design. The Russian / Maltese monogram was added and the image of the
Imperial eagle was radically changed to closely resemble that of the
Prussian Army. This banner could have belonged to any of the three
Life-Guards' Regiments existent during the reign of Paul I: the
Preobrazhensky, Semyonovsky, or Izmailovsky, since all Life-Guards'
Regiments received the same type of banner, differentiated only by the
colors of their poles. Prior to Paul I's accession to the throne, each
new Russian monarch would discard the army's existing regalia in order
to substitute designs pleasing to the new ruler. Paul definitively
changed this rule, declaring that all flags and banners were to remain
in service indefinitely. It is therefore possible that the offered lot
was in use well after Paul's assassination in 1801, and even during
the battles of the Napoleonic Wars of 1805-1814.
On this design, see A.V. Viskovatov, Istoricheskoe opisanie odezhdy i
vooruzheniia rossiiskikh voisk, vol. 9, St. Petersburg, 1841-1862,
ill. 1257 and V.V. Zvegintsov, Znamena i Shtandarty Russkoi Armii,
Paris, 1964, p. 25.William Garrison, 03 January 2013

Looking like original banner of 1800... In 1800 this type of banners was
granted to 3 regiments. Full amount of banners - 47: 19 - to Life-Guard
Preobrazhensky Regiment, 14 - to Life-Guard Semenovsky Regiment, 14 - to
Life-Guard Izmailovsky Regiment.Victor Lomantsov, 04 January 2013

Personal Standard of the Tsar in Moscow
(1693-1699)

image by Arnaud Palac and António Martins, 12 Dec 1999

The Tsar’s standard in Moscow
is the same as the normal one but
white, blue, red horizontal stripes background.Jaume Ollé, 21 Jul 1998

I’m not so sure it is the one. The eagle should be yellow
and not black with maps (“naval version”).
Russian tricolour with golden coat of arms allover:
The first vessel standard "Moscow Tsar Flag" (1693-1699).Željko Heimer, 03 Apr 1999, summarizing from
Flag-znamya korablya,
Russian Navy website, consulted 07 Mar 1999

Symbolism of Andreevsky Flag
was also Peter’s contribution to his father — tsar Alexei
Mikhailovich who instituted the special flag - dark red
two-headed eagle on white-blue-red cloth — for the first
military Russian vessel — three-mast galiot Eagle.Edward Mooney, 14 Mar 1999, quoting from
Russian
Navy website

In one of the worlds first flagbooks, compiled
by Carel Allard (from Amsterdam) in 1695
[ala95],
shows three Russian flags:

horizontal white-blue-red, over all (shifted
to the hoist) a golden double headed eagle with
a red shield (with St.George, without the dragon)
on its chest and a golden crown over its heads.
Caption: Czar of Moscovia.

horizontal white-blue-red, over all a blue
saltire. Ratio of the flag aprox. 1:3. Caption:
Other flag of Czar of Moscovia.
(See here.)

Flag for “The Alexandria”, a personal summer-cottage of
Emperor. White flag with arms: Azure, a Sword in pale Argent hilted Or
and decored with a round Wreath of flowers and leaves.Victor Lomantsov, 20 Jul 2000

Flags of Ivan IV, “the terrible”

image by António Martins, 22 Jan 2003,
from The Cultural Atlas of Russia

I have book called The Cultural Atlas of Russia which shows a
flag of Ivan VI which is called the flag at Kazan.Steve Stringfellow, 23 and 27 Aug 1999

It is a dark top heavy trapezoid, with the refered icon painted on the
hoist part and a roughly regular arrangement of light five stars and two
couped crosses on the tappering fly. As said, the now faded colors are
disputed (it is a black-and-white photo).António Martins, 21 Jan 2003

This flag is totally different than the one in Smith’s 1975 big book
[smi75c]. So, the question is: what flag
did Ivan IV have?Steve Stringfellow, 23 and 27 Aug 1999

I confess that I have no idea: Ivan the terrible was the first
Muscovy prince to use the title of Tsar
(from latin "CAESAR", in russian "carh |
царь"), after
geting rid of Mongol / Tatar domination
and having submitted to his own personal power the other russian princes
(Tver, Kiev,
Novgorod, etc.) — hence «Tsar
of all Russias». This happend in a historical period
when heraldry wasn’t yet really set in Russia (it come somewhat
later, after italian, german and french
influences), and I guess that Ivan’s flag would have much more to do
with mongol Khan’s regalia, than to the usual symbols of a westerner
monarch. This image seems to confirm it.António Martins, 24 Aug 1999

Ivan IV, the Terrible (1530-1584), often considered as the founder of the
modern Russian Empire. He was the first to adopt the title of czar (from
Latin Caesar, since Moscow was supposed to be the third Rome —
replacing Rome and Byzance) and increased the Russian territory by conquering
the khanates of Kazan and
Astrakhan.Ivan Sache, 01 Oct 2000